If you don't want them to be visible you can tell ubuntu not to mount them. But if it is for security that you don't want then to be seen by ubuntu, then you need to add security at the MS-Windows end.
–
richardJul 17 '14 at 16:46

2 Answers
2

Linux can read (and write) to many filesystems, including ntfs, which is likely how your windows partitions are formatted. Many OS installers (including Ubuntu apparently) will scan your disks for any partitions that Linux knows how to mount, and set those up to be mounted at boot, which is why you can access them.

Ubuntu is capable of reading and writing files stored on Windows formatted partitions. These partitions are normally formatted with NTFS, but are sometimes formatted with FAT32. You will also see FAT16 on other devices.

General Considerations

Ubuntu will show files and folders in NTFS/FAT32 filesystems which are hidden in Windows. Consequently, important hidden system files in the Windows C:\ partition will show up if this is mounted. Since it is all-too-easy to accidentally modify or delete files which are essential for Windows, it is advisable to mount your Windows C:\ partition as seldom as possible, preferably not at all, or read-only by configuring /etc/fstab (see below). If you have data which you want to access regularly from both Windows and Ubuntu, it is better to create a separate data partition for this, formatted NTFS.

Whether you write to your Windows C:\ partition or a shared NTFS data partition, be aware that if you are using Windows 7, and Windows 7 is in a hibernated state when you write to the NTFS partition from Ubuntu, you will lose all your changes. This is because when Windows 7 is hibernated it writes the system state to a file stored on disk and restores from that file when the system is re-awakened, thus restoring the whole fileystem to a state before any changes made from Ubuntu. In Windows 7 you must avoid using hibernation. With Windows 8, the situation is more complex in that, by default, it uses a hybrid hibernation/shutdown when you shut the system down. Any changes made by Ubuntu will be lost when you reboot into Ubuntu.

With both Windows 7 and Windows 8 (when installed to a legacy mbr partition table) there is usually a 100-200MB boot partition labelled "SYSTEM". Do not mount it - you do not need to. Similarly it is highly advisable to leave any recovery partitions unmounted.